Preheat the oven to 350 F, and spray a 9x13-inch baking dish with cooking spray.
Cook the penne pasta until al dente according to package directions. Drain and reserve.
In a large bowl, combine the cooked pasta, black beans, whole kernel corn, taco seasoning, cumin, red pepper flakes, shredded chicken, and tomatoes.
Spoon the mixture into the baking dish and top with the shredded cheeses.
Cover with foil and bake for 35 minutes, removing the foil after 20 minutes.